Name: Chryseomicrobium excrementi ET03
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 159857

Type strain:

Species: Chryseomicrobium excrementi

Strain Designation: ET03

Culture col. no.: KCTC 33943, LMG 30119, JCM 32415, MCC 3378

Strain history: <- Ranadhir Chakraborty, Univ. of North Bengal

NCBI tax ID(s): 2041346 (species)

Section

Chryseomicrobium excrementi ET03 is an aerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from cast of an earthworm .

colony-forming
Gram-positive
rod-shaped
spore-forming
aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Caryophanaceae*
	Genus	*Chryseomicrobium*
	Species	**Chryseomicrobium excrementi**
	Full Scientific Name (LPSN)	Chryseomicrobium excrementi Saha et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #66561]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #66561]	Cell length	1.0-2.0 µm

[Ref.: #66561]	Cell width	0.5 µm

[Ref.: #66561]	Cell shape	rod-shaped

[Ref.: #66561]	Motility	no

[Ref.: #66561]	Colony color	golden yellow
[Ref.: #66561]	Colony shape	circular
[Ref.: #66561]	Incubation period	<1 day
[Ref.: #66561]	Cultivation medium used	LB agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #66561]

Culture medium

LB (Luria-Bertani) agar

[Ref.: #66561]

Culture medium growth

		Temperature
[Ref.: #66561]	growth	20-40 °C
[Ref.: #66561]	optimum	35-37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #67771]	growth	37 °C

[Ref.: #66561]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #66561]			optimum	7
[Ref.: #66561]			growth	6-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #66561]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #66561]

Ability of spore formation

yes

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66561]		NaCl		growth	0-8	%
[Ref.: #66561]		NaCl		optimum	2	%

[Ref.: #67770]

Observation

quinones: MK-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66561]	(R)-malic acid ChEBI	-	assimilation
[Ref.: #66561]	(S)-lactate ChEBI	-	assimilation
[Ref.: #66561]	2-oxoglutarate ChEBI	-	assimilation
[Ref.: #66561]	3-O-methyl-D-glucose ChEBI	+	assimilation
[Ref.: #66561]	4-aminobutyrate ChEBI	-	assimilation
[Ref.: #66561]	acetic acid ChEBI	+	assimilation
[Ref.: #66561]	acetoacetate ChEBI	+	assimilation
[Ref.: #66561]	bromosuccinate ChEBI	-	assimilation
[Ref.: #66561]	cellobiose ChEBI	-	assimilation
[Ref.: #66561]	cellobiose ChEBI	-	builds acid from
[Ref.: #66561]	citric acid ChEBI	-	assimilation
[Ref.: #66561]	D-arabitol ChEBI	+	assimilation
[Ref.: #66561]	D-aspartate ChEBI	-	assimilation
[Ref.: #66561]	D-fructose ChEBI	+	assimilation
[Ref.: #66561]	D-fructose 6-phosphate ChEBI	-	assimilation
[Ref.: #66561]	D-fucose ChEBI	-	assimilation
[Ref.: #66561]	D-galactose ChEBI	-	assimilation
[Ref.: #66561]	D-galacturonic acid ChEBI	-	assimilation
[Ref.: #66561]	D-glucarate ChEBI	-	assimilation
[Ref.: #66561]	D-gluconate ChEBI	+	assimilation
[Ref.: #66561]	D-glucose 6-phosphate ChEBI	+	assimilation
[Ref.: #66561]	D-glucuronate ChEBI	-	assimilation
[Ref.: #66561]	D-mannitol ChEBI	-	assimilation
[Ref.: #66561]	D-mannose ChEBI	-	assimilation
[Ref.: #66561]	D-serine ChEBI	-	assimilation
[Ref.: #66561]	D-sorbitol ChEBI	-	assimilation
[Ref.: #66561]	formate ChEBI	-	assimilation
[Ref.: #66561]	fructose ChEBI	+	builds acid from
[Ref.: #66561]	galactarate ChEBI	-	assimilation
[Ref.: #66561]	gelatin ChEBI	-	assimilation
[Ref.: #66561]	gelatin ChEBI	+	hydrolysis
[Ref.: #66561]	gentiobiose ChEBI	-	assimilation
[Ref.: #66561]	glucose ChEBI	+	builds acid from
[Ref.: #66561]	glucuronamide ChEBI	-	assimilation
[Ref.: #66561]	glycerol ChEBI	-	assimilation
[Ref.: #66561]	glycine-proline ChEBI	-	assimilation
[Ref.: #66561]	inosine ChEBI	-	assimilation
[Ref.: #66561]	inulin ChEBI	-	builds acid from
[Ref.: #66561]	L-alanine ChEBI	-	assimilation
[Ref.: #66561]	L-aspartate ChEBI	+	assimilation
[Ref.: #66561]	L-fucose ChEBI	-	assimilation
[Ref.: #66561]	L-glutamate ChEBI	+	assimilation
[Ref.: #66561]	L-histidine ChEBI	-	assimilation
[Ref.: #66561]	L-malate ChEBI	+	assimilation
[Ref.: #66561]	L-pyroglutamic acid ChEBI	+	assimilation
[Ref.: #66561]	L-rhamnose ChEBI	+	assimilation
[Ref.: #66561]	L-serine ChEBI	-	assimilation
[Ref.: #66561]	lactose ChEBI	-	assimilation
[Ref.: #66561]	maltose ChEBI	+	builds acid from
[Ref.: #66561]	mannose ChEBI	-	builds acid from
[Ref.: #66561]	melibiose ChEBI	-	assimilation
[Ref.: #66561]	melibiose ChEBI	-	builds acid from
[Ref.: #66561]	methyl (R)-lactate ChEBI	-	assimilation
[Ref.: #66561]	methyl D-glucoside ChEBI	-	assimilation
[Ref.: #66561]	methyl pyruvate ChEBI	-	assimilation
[Ref.: #66561]	myo-inositol ChEBI	+	assimilation
[Ref.: #66561]	N-acetylgalactosamine ChEBI	-	assimilation
[Ref.: #66561]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #66561]	n-acetylneuraminate ChEBI	-	assimilation
[Ref.: #66561]	nitrate ChEBI	+	reduction
[Ref.: #66561]	pectin ChEBI	-	assimilation
[Ref.: #66561]	propionate ChEBI	-	assimilation
[Ref.: #66561]	quinate ChEBI	+	assimilation
[Ref.: #66561]	raffinose ChEBI	-	assimilation
[Ref.: #66561]	salicin ChEBI	+	assimilation
[Ref.: #66561]	salicin ChEBI	+	builds acid from
[Ref.: #66561]	stachyose ChEBI	-	assimilation
[Ref.: #66561]	starch ChEBI	-	hydrolysis
[Ref.: #66561]	sucrose ChEBI	-	assimilation
[Ref.: #66561]	sucrose ChEBI	-	builds acid from
[Ref.: #66561]	trehalose ChEBI	-	assimilation
[Ref.: #66561]	trehalose ChEBI	-	builds acid from
[Ref.: #66561]	turanose ChEBI	-	assimilation
[Ref.: #66561]	tween 40 ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #66561]	1 % sodium lactate		yes
[Ref.: #66561]	aztreonam ChEBI		yes
[Ref.: #66561]	D-serine ChEBI	yes
[Ref.: #66561]	fusidate ChEBI	yes
[Ref.: #66561]	guanidinium chloride ChEBI	yes
[Ref.: #66561]	lincomycin ChEBI	yes
[Ref.: #66561]	lithium chloride ChEBI		yes
[Ref.: #66561]	minocycline ChEBI	yes
[Ref.: #66561]	nalidixic acid ChEBI		yes
[Ref.: #66561]	niaproof ChEBI	yes
[Ref.: #66561]	potassium tellurite ChEBI		yes
[Ref.: #66561]	sodium butyrate ChEBI		yes
[Ref.: #66561]	tetrazolium blue ChEBI	yes
[Ref.: #66561]	troleandomycin ChEBI	yes
[Ref.: #66561]	vancomycin ChEBI	yes
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #66561]		acetoin ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #66561]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #66561]	catalase	-	1.11.1.6
[Ref.: #66561]	cytochrome oxidase	-	1.9.3.1
[Ref.: #66561]	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #66561]

Fatty acid	Percentage
C15:0 iso	45
C16:1 w7c OH	13
C16:0 iso	11.8
C14:0 iso	6.2
C15:0 anteiso	3.4
C17:0 iso	2.2
C16:0	1.8
C17:0 anteiso	1.6
C16:1 w11c	1.2
C17:1 iso / C17:1 anteiso	0.9
C16:1 w7c / C16:1 w6c	0.6
C14:0	0.5

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #66561]	Sample type/isolated from	cast of an earthworm (Eisenia fetida)
[Ref.: #66561]	Geographic location (country and/or sea, region)	Centre of Floriculture and Agribusiness Management of University of North Bengal at Siliguri, West Bengal
[Ref.: #66561]	Country	India
[Ref.: #66561]	Country ISO 3 Code	IND
[Ref.: #66561]	Continent	Asia
[Ref.: #66561]	Geographic location	26.7072°/88.3558°
[Ref.: #66561]	Enrichment culture	LB agar
[Ref.: #66561]	Enrichment culture duration	over night

[Ref.: #67770]	Sample type/isolated from	Cast of an earthworm (Eisenia fetida) reared at the Centre of Floriculture and Agribusiness Management of University of North Bengal at Siliguri
[Ref.: #67770]	Host species	Eisenia fetida
[Ref.: #67770]	Geographic location (country and/or sea, region)	West Bengal
[Ref.: #67770]	Country	India
[Ref.: #67770]	Country ISO 3 Code	IND
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From freshly liberated cast of Eisenia fetida, Campus area of University of North Bengal
[Ref.: #67771]	Geographic location (country and/or sea, region)	Siliguri, West Bengal
[Ref.: #67771]	Country	India
[Ref.: #67771]	Country ISO 3 Code	IND
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU230523 (>99% sequence identity) for Planococcaceae from Microbeatlas

Aquatic Samples	124
Soil Samples	56
Animal Samples	360
Plant Samples	6
Total Samples	546

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Bacterium ET3(2016) 16S ribosomal RNA gene, partial sequence	KU230523	1517	ENA	2041346 tax ID
[Ref.: #66561]	Bacterium ET3(2016) 16S ribosomal RNA gene, partial sequence	KU230523.2	1517	ENA	2041346 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Chryseomicrobium excrementi ET03	GCA_002798305	scaffold	GenBank	2041346 tax ID
[Ref.: #66792]	Chryseomicrobium sp. ET03	2041346.3	wgs	PATRIC	2041346 tax ID	*
[Ref.: #66792]	Chryseomicrobium excrementi ET03	2882380101	draft	JGI IMG/M	2041346 tax ID	*

[Ref.: #66561]	GC-content	42.90 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	42.9 mol%	genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Chryseomicrobium excrementi ET03 NCBI: GCA_002798305.1
[Ref.: #69481]	spore-forming	yes	88	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Chryseomicrobium sp. ET03 PATRIC: 2041346.3
[Ref.: #69480]	motile	yes	73.842	no
[Ref.: #69480]	gram-positive	yes	90.318	yes
[Ref.: #69480]	anaerobic	no	98.474	yes
[Ref.: #69480]	aerobic	yes	92.12	yes
[Ref.: #69480]	halophile	yes	51.189	no
[Ref.: #69480]	spore-forming	yes	75.66	yes
[Ref.: #69480]	glucose-util	yes	80.045	no
[Ref.: #69480]	flagellated	no	57.971	yes
[Ref.: #69480]	thermophile	no	99.738	yes
[Ref.: #69480]	glucose-ferment	no	91.327	no

Availability in culture collections External links

[Ref.: #66561]

Culture collection no.

KCTC 33943, LMG 30119, JCM 32415, MCC 3378

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chryseomicrobium excrementi sp. nov., a Gram-stain-positive rod-shaped bacterium isolated from an earthworm (Eisenia fetida) cast.	Saha T, Chakraborty B, Das S, Thakur N, Chakraborty R	Int J Syst Evol Microbiol	10.1099/ijsem.0.002791	2018	*

References

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#66561

Tilak Saha, Biswanath Chakraborty, Sayak Das, Nagendra Thakur and Ranadhir Chakraborty: Chryseomicrobium excrementi sp. nov., a Gram-stain-positive rod-shaped bacterium isolated from an earthworm (Eisenia fetida) cast. IJSEM 68: 2165 - 2171 2018 ( DOI 10.1099/ijsem.0.002791 , PubMed 29749923 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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Chryseomicrobium excrementi ET03

Chryseomicrobium sp. ET03

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